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170 related items for PubMed ID: 24729761

  • 1. Extension of UNRES force field to treat polypeptide chains with D-amino-acid residues.
    Sieradzan AK, Hansmann UH, Scheraga HA, Liwo A.
    J Chem Theory Comput; 2012 Nov 13; 8(11):4746-4757. PubMed ID: 24729761
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  • 3. Physics-based potentials for the coupling between backbone- and side-chain-local conformational states in the UNited RESidue (UNRES) force field for protein simulations.
    Sieradzan AK, Krupa P, Scheraga HA, Liwo A, Czaplewski C.
    J Chem Theory Comput; 2015 Feb 10; 11(2):817-31. PubMed ID: 25691834
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  • 5. A general method for the derivation of the functional forms of the effective energy terms in coarse-grained energy functions of polymers. I. Backbone potentials of coarse-grained polypeptide chains.
    Sieradzan AK, Makowski M, Augustynowicz A, Liwo A.
    J Chem Phys; 2017 Mar 28; 146(12):124106. PubMed ID: 28388107
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  • 6. Determination of effective potentials for the stretching of C(α) ⋯ C(α) virtual bonds in polypeptide chains for coarse-grained simulations of proteins from ab initio energy surfaces of N-methylacetamide and N-acetylpyrrolidine.
    Sieradzan AK, Scheraga HA, Liwo A.
    J Chem Theory Comput; 2012 Apr 10; 8(4):1334-1343. PubMed ID: 23087598
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  • 7. An improved functional form for the temperature scaling factors of the components of the mesoscopic UNRES force field for simulations of protein structure and dynamics.
    Shen H, Liwo A, Scheraga HA.
    J Phys Chem B; 2009 Jun 25; 113(25):8738-44. PubMed ID: 19480420
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  • 8. Determination of side-chain-rotamer and side-chain and backbone virtual-bond-stretching potentials of mean force from AM1 energy surfaces of terminally-blocked amino-acid residues, for coarse-grained simulations of protein structure and folding. II. Results, comparison with statistical potentials, and implementation in the UNRES force field.
    Kozłowska U, Maisuradze GG, Liwo A, Scheraga HA.
    J Comput Chem; 2010 Apr 30; 31(6):1154-67. PubMed ID: 20017135
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  • 16. Toward Consistent Physics-Based Modeling of Local Backbone Structures and Chirality Change of Proteins in Coarse-Grained Approaches.
    Lipska AG, Sieradzan AK, Atmaca S, Czaplewski C, Liwo A.
    J Phys Chem Lett; 2023 Nov 09; 14(44):9824-9833. PubMed ID: 37889895
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  • 17. Improvement of the treatment of loop structures in the UNRES force field by inclusion of coupling between backbone- and side-chain-local conformational states.
    Krupa P, Sieradzan AK, Rackovsky S, Baranowski M, Ołldziej S, Scheraga HA, Liwo A, Czaplewski C.
    J Chem Theory Comput; 2013 Oct 08; 9(10):. PubMed ID: 24273465
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  • 18. Extension of the force-matching method to coarse-grained models with axially symmetric sites to produce transferable force fields: Application to the UNRES model of proteins.
    Liwo A, Czaplewski C.
    J Chem Phys; 2020 Feb 07; 152(5):054902. PubMed ID: 32035448
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  • 19. All-Atom Internal Coordinate Mechanics (ICM) Force Field for Hexopyranoses and Glycoproteins.
    Arnautova YA, Abagyan R, Totrov M.
    J Chem Theory Comput; 2015 May 12; 11(5):2167-2186. PubMed ID: 25999804
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  • 20. Torsional potential of 4,4'-bipyridine: ab initio analysis of dispersion and vibrational effects.
    Pérez-Jiménez AJ, Sancho-García JC, Pérez-Jordá JM.
    J Chem Phys; 2005 Oct 01; 123(13):134309. PubMed ID: 16223290
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